There is a need for faster nucleic acid sequencing. Although small fragments of nucleic acids (i.e. about 1000 bases) may be sequenced on a time scale of hours, the sequencing of entire genomes can increase the sequencing time by many orders of magnitude. Existing nucleic acid sequencing methods may be direct (i.e., each base is determined) or indirect (i.e., smaller sequences within a larger sequence are determined and then assembled to reveal the larger sequence). However, current methods such as those that rely on arrays of oligonucleotide probes have made relatively limited progress in decreasing sequencing time. Accordingly, there is a need for improved sequencing methods that increase sequencing throughput.